If a vendor makes PayPal purchases slightly more expensive, it can cause bad will with the customer (who is less likely to return and make more purchases). Exceptions are sometimes with one-off purchases (e.g. a conference ticket or course fee).
Separately, the original comment asserted that the PayPal account charges you each transaction (which is false). The new argument is different, which asserts that a vendor may charge you more due to PayPal fees.